Contamination Isolation
by twindragonsx1
Summary: A deadly plague sweeps the nation of Equestria, transforming its citizens into mindless, rotting, animated corpses. The neighboring nations have closed off their borders, effectively trapping survivors of the plague within the country. Now, it's up to Twilight Sparkle and her friends to protect those that are left and find a cure, before time runs out. AU. Humanized.
1. Prologue- Infection

**(A/N: New story. Centers around zombie-killing action. 'Nuff said.**

**Reviews appreciated. Flames will be used to roast the infected.**

_**Contamination Isolation**_

Prologue

_Infection_

The infection started in Manehattan.

What was originally supposed to be a be a cure for the deadly disease known as AIDS turned out to be another highly infectious disease, with near-100% mortality rates.

At first, when the disease was still in the preliminary stages of testing against AIDS, it was a non-lethal liquid, taken by injection. But as time wore on, more chemical reagents were added, thus allowing the so-called "cure" to be transmitted by the air.

The scientists working on the disease had recently hired a novice chemical handler, and when the said handler was introduced to a sample of the disease to work on, he accidentally knocked a flask of a highly-reactive reagent into it.

The novice was blissfully unaware of the new compound he had created, and when a test subject infected with AIDS was injected with it, his condition was cured. All traces of AIDS had been removed from his system.

The cured patient was kept in isolated containment for a few more weeks to ensure that no side effects or ill-desired symptoms appeared. But as the days passed, the patient began to complain of pain originating from his abdominal region. He was screened for any other diseases or anything that could have caused the pain, but nothing was found. Soon came the throbbing headaches, which, in turn, turned into migraines. Nausea and diarrhea followed shortly afterwards. Hallucinations became frequent, and the patient expired in his sleep a day after the "side effects" were reported.

His body re-animated in his quarters the following morning.

Tapes were reviewed from the cameras in his quarters. The footage showed that in the two hours since the patient expired, his skin had rapidly deteriorated, turning a mottled grey at first, then peeling, and soon, entire chunks of flesh had fallen off of his body. Most of the patient's teeth had fallen out, and those that remained were yellowed and decayed. He had been beating on the wall for hours, showing that his physical strength had doubled by over 200%, as evident by the damage done to the wall.

Armed guards were sent in to dispose of the re-animated corpse. Once the doors opened, the guards began to file in. The thing had been facing away from them.

And before the guards could react, the corpse was upon them, feeding on the unfortunate guard who had made the mistake of standing the closest. The other guards were too paralyzed with shock, disgust and fear to do anything as blood, flesh, and innards flew, painting the walls around them red.

Once the corpse finished its meal, it advanced with great speed towards the next guard. The group opened fire upon the rotting corpse. The corpse continued moving, seemingly absorbing rounds like a sponge. It lunged and bit down upon its prey's throat, ripping it open and spraying blood everywhere. The other guards had not stopped firing, and they ceased once one of the guards finally marched up to the corpse, pulled out his sidearm, put the barrel against the bare skull, and pulled the trigger.

Infected blood flew everywhere, and as the men screamed, it got into their mouths.

And just about two hours later, they turned.

The facility was placed on lockdown, and as the scientists struggled to survive against the onslaught of the Infected, the containers holding the gaseous form of the disease was released. Even as the survivors barricaded themselves within the facility, they had already been infected. The airborne disease spread outside of the facility it had once been housed in.

As any good leader would do, Her Royal Majesty, Princess Celestia sent her own guards into the facility with the authorization to eliminate anything that moved.

Unbeknownst to the guards, or even the wise Princess herself, the Infected had already moved out of the facility and into the surrounding areas.

And from there, they moved into the city, infecting hundreds, if not thousands.

Quickly, reports of "cannibalism" reached the other cities, and the Princess sent a team of Royal Guards to the scene.

Just hours upon their arrival, all contact with the team was lost. Their final message spoke of heavily decayed corpses feeding upon and infecting the living.

From there, the entirety of the Royal Guard mobilized to neutralize any threat in Manehattan. The Elements of Harmony and their loved ones were moved into Canterlot for safety.

However, even as all these precautions were taken, the disease, still airborne, had infected the entire city of Fillydelphia. Soon, the city was filled with the Infected, hungry for the flesh of the living. More Royal Guards were dispatched to repel the Infected in Fillydelphia.

Within a week's time, the cities of Vanhoover, Detrot, and Las Pegasus had fallen, and the surviving Royal Guards were recalled to Canterlot.

Most surviving civilians were relocated to the city above the clouds known as Cloudsdale, which was considered a safe zone from the surmounting apocalypse down on the ground.

The citizens of Equestria couldn't have been more wrong.

Somehow, through all the screening of the flights bound to Cloudsdale, a single infected woman had managed to board an aircraft. She turned while the flight was in transit, and when the plane was infected, the pilot made the decision to land at Cloudsdale International Airport. Squadrons of Equestrian Royal Air Force air-superiority fighters were deployed in a fruitless attempt to shoot down the incoming aircraft.

The passenger aircraft went down in flames; however, it did not plummet back down to the land as intended. Instead, it collided with the runway, rolling and tumbling, until it smashed through the wall of a hangar.

Sure enough, the Infected came running out of the destroyed building, sprinting towards the terminals that held so many civilians.

With so many potential hosts, the Infected breached the perimeter that had been hastily erected in front of the terminals. The wave of undead swept past them and into the terminals.

Hours later, reports were received that the once-splendid city in the skies, Cloudsdale, had fallen to the Infected.

Some of the Infected had traveled from the northern cities and into the Everfree Forest, emerging out from the other side into a town known as Ponyville.

The residents of Ponyville, with no access to many ranged weapons, and with the Canterlot Royal Guards unwilling to assist them, were easily devoured or infected within a single day.

Isolated from all sides, Canterlot was made easy prey for the undead. With the knowledge that small pockets of the living still fending off the Infected were present in all the major cities, the Royal Council, as per unanimous vote, had decided to move both Princesses, the Elements of Harmony, and their families into a shelter held by a pocket of resistance in Manehattan, the city where it all started.

Just hours after their relocation, Canterlot came under siege by waves of the Infected. Most of the city was lost after the attack, but one large fortress still remained under living control: Canterlot Castle, along with the surrounding areas.

Even as the world around them crumbled to dust, the survivors pushed on.

And here is where we follow the tale of the young Element Bearer Twilight Sparkle as she and her friends struggle to uncover the secrets of a disease that none have ever seen the likes of before…

Because remember: in a world filled with the Infected, friendship becomes just as dead as they do.

**(A/N: Well, how did I do so far? I'm not sure if this story will be enjoyed, but I want to give it a shot. I've read some of the MLP/Zombie fanfics, and some of them are good. Some of them are not. So I wanted to finally give a go at creating a good one. **

**This is really just the epilogue, so this part will be a little shorter than all the other chapters.**

**Be sure to check out my other stories!**

**Reviews would be very much appreciated, and flames will be used to keep the Infected at bay.**

**Until next time,**

**-twindragonsx1**

**Devin)**


	2. Chapter 1- Nightmare Escape

**(A/N: Alright, here's where the real action starts.**

**I apologize for the long wait, as I have been busy lately.**

**If you spot typos, please ignore them, as a majority of the chapter was written well after midnight, and I simply don't have the time to look over the chapter.**

**Note that the scenes that take place are not intended RariJack or Flash Sentry/Twilight Sparkle scenes. Feel free to take them as such, however. Do **_**NOT**_** fanboy/girl over them in the reviews section, please.**

**No, the swarm of Infected in this portion of the chapter is not like in **_**World War Z**_**, where they create massive dog piles and trample each other. That comes later. This swarm is more like in **_**Call of Duty: Black Ops I/II Zombies**_**.**

**Lastly, I would once again like to mention my friend "A Derpy King Boo" in this author's note. He has many good stories posted, and I recommend looking at them.**

**Reviews would be appreciated. Flames will be used to put down the Infected.)**

_**Contamination Isolation**_

Ch. 1

_Nightmare Escape_

Twilight Sparkle whirled around as a hand grenade flew past her head. She waited for a few seconds, heard the explosion, and turned back around, raising her rifle.

Before her lay the bloody mess that was the battlefield. Men and women fought those that had risen once again, hungering for human flesh. Beside her was Rainbow Dash, who currently was letting loose a volley of gunfire from her rifle. Bullets and grenades flew overhead as the Infected attempted to smash down the barricades that separated them from the survivors and the bunker.

Twilight let five bursts of concentrated fire out from her rifle.

"Keep firing!" she said. "We need to keep them away from the bunker!"

She pulled a flare off of her belt. Igniting it, she threw it at the mass of undead in front of her.

Ducking down behind her cover, Twilight pulled a radio from her belt, pushing a button on it and bringing it up to her ear. "Give me an airstrike, now!"

On the other end of the radio, Spitfire, captain of the (formerly) famous flying team know as the Wonderbolts, answered. "Roger that. ETA ten minutes."

"Not good enough!" Twilight shouted. "Be here in five!" She winced as a rocket from Pinkie Pie's launcher exploded amongst the packed undead.

Spitfire sighed. "Alright. Just hang on." From there, Spitfire switched her radio off. "Alright, people, gear up! We fly in five!" She approached the maintenance chief. "I need one-fifty pound bombs mounted on our planes by the time I get out here. Got it? Good." Spitfire turned and began heading towards the pilots' ready rooms, not giving the chief time to say anything.

Applejack watched from the roof of the bunker as the crowd of the Infected steadily approached the barricades that were set up not far from her vantage point. She turned to her left, seeing her older brother approaching, hefting his heavy Gatling gun. She nodded as he came to rest beside her.

Big Macintosh set up his gun, mounting it on the wall, and loaded it. Once finished, he did not hesitate to pull the trigger.

"Where's my Celestia-damned air support!?" Twilight screamed over the roar from Big Macintosh's gun from overhead.

And as if on cue, her radio flared to life. "Air support inbound. Minimum safe distance is two-hundred meters. Move, now," the voice of Captain Spitfire crackled through.

"Move, everyone! Get back about two-hundred meters! Go!" Twilight barked orders.

The Defenders moved back, letting the mounted guns on the roof of the bunker handle the undead. Once back at the same distance of two hundred meters, they stopped, turned around and continued firing.

Twilight gaped up as the F/A-18-F Super Hornet aircraft flew overhead. They dove sharply, releasing their bombs as they did so, and nosed up, turning around and heading back to base.

Rainbow Dash held her breath and looked away as the bombs dropped. She was rewarded with a massive, fiery explosion, followed by another and two more after that. She turned to look again, only to see that only about a quarter of the undead horde had been vaporized by the blasts.

"Shit…" she muttered. The undead swarm kept coming. In fact, it looked as if they came _faster_ than before.

The mass of cold bodies smashed through the abandoned remains of the barricades, and neared the hill on which the bunker sat atop of with little or no resistance. The many rounds fired into the crowd did nothing to mitigate their numbers.

"We can't hold them back any longer!" Rainbow Dash said to Twilight. "If we stay here, we'll be just as dead as they are!"

Twilight looked at the amount of men defending the bunker and the horde of undead steadily approaching from the south. She glanced up at the cloudy grey skies above them, and finally said, "You're right. Come on everyone! Let's move! Get into the bunker! I want those bulkhead doors closed in five!"

The men and women defending the gates did not hesitate. They struggled and pushed their way into the bunker. But it was not enough. The wave of undead crashed into the bunker, trapping many Defenders outside. And one of them was Rainbow Dash.

"Rainbow!" Twilight screamed.

"Go! Get the doors closed!" Rainbow shouted back. She kicked one of the Infected that had lunged at her. "And one last thing!"

Twilight looked at her. "Yes?"

Rainbow turned around and looked at Twilight. "Tell Scoots that I'll miss her." With that, Rainbow turned around and continued the futile fight.

Hesitantly, Twilight nodded. She threw the lever that sealed the bulkhead door. Alarms wailed as a red light encompassed the airlock and the occupants inside. As the doors shut, the last thing Twilight saw were the trapped Defenders, surrounded and heavily outnumbered, being overcome by the undead.

That included one of her friends, Rainbow Dash.

On the bunker roof, fear flooded Applejack's body as the Infected began to throw themselves against the hard grey bricks that made up the bunker walls. The undead piled themselves up against the walls, creating columns of bodies that steadily rose to the roof. She began to panic as the cold, rotting hands reached over the edges of the roof, and the Infected began to haul themselves up.

She looked towards her older brother. If he was scared, he showed no signs of it.

"Come on, Big Mac," Applejack said. "Come on! We can't stay here!"

"Eeyup," he replied as he began to pack up his gun.

Applejack whipped out her shotgun from her back and aimed towards the first set of grey, mottled hands that she saw were grasping for a hold on the stone roof.

Finally, Big Macintosh had picked up his gun and grabbed his sister by the shoulders and began to run towards the steel door that gave access to the roof.

Just as they reached it, the Infected pulled themselves over the edge and sprinted towards the two siblings.

Applejack looked over her shoulder while she ran. Aiming her shotgun, she shot the closest corpse to her. Looking to her left, she shot two more. A third corpse lunged at her from her right. Applejack tossed the shotgun away and drew the revolver holstered on her waist. She aimed and pulled the trigger.

Back down below, blood and gore flew and splattered the people nearest to the doors as the bulkheads sealed. There was a moment of silence to honor the now-deceased Defenders, as well as to see if the undead even attempted to break down the closed doors.

Pinkie Pie, who was standing next to Twilight, sighed. She stood there for a minute, until she noticed that Rainbow Dash was absent.

"Wait, where's Dashie?" she asked no one in particular.

Murmurs moved about the crowd of gathered Defenders as they searched for the Defender captain in question.

Quietly, Twilight said, "She was one of the many that was trapped outside when the doors shut."

Another moment of stunned silence in grieving for their fallen captain descended amongst the crowd.

"But… but… I saw her," Pinkie stammered.

"So did I," Twilight replied. "So did I…"

Pinkie was quiet for another few seconds until she began to weep silently. She collapsed onto the cold, hard cement below her feet, the tears staining the grey stone. Two other Defenders knelt down and comforted her.

"Come on everyone. I know you're tired and still in shock from the loss of many good friends and fighters. Let's get-"Twilight was unable to finish, cut off by the sound of stressed and dented metal.

Everyone was quiet as the sound of flesh against steel reverberated throughout the room.

The steel bulkhead groaned and dented as the Infected hurled themselves against it, desperately trying to gain access to the complex.

"Everyone OUT!" Twilight screamed. "Get into the more defendable sectors of the bunker! Fight to the last man or woman! Get the Princesses and the civilians out first! Escort everyone to the airfield, and tell the Wonderbolts to prepare their aircraft for evacuation departure! If the airfield is not feasible to retreat, then use the emergency exit and get as far away as possible from the bunker!"

The assembled Defenders sprang into action, opening the doors that led into the bunker. Splitting up, they did as they were ordered.

Twilight and Pinkie made their way to the closest equipment locker they could find, stocking up on ammunition and other equipment.

"Do you really think we'll make it out alive, Twilight?" Pinkie asked.

For just a moment, Twilight was silent. Then, she spoke, "I don't know, but I will give my life for everyone else if it means their survival."

Applejack and Big Mac rushed down the stairs that led into the bowels of the bunker. When they finally got to the gateway to the airfield, they stopped, shutting the door that led to the roof.

"Big Mac, block the door that goes to the roof," Applejack said. He moved to comply, pushing chairs and tables to barricade the door (not that it would matter, anyways).

People began pouring out of the doors that led to the living quarters of the bunker, afraid and confused.

"Come on, y'all, get to the evacuation choppers! Go!" Reluctantly, the civilians moved to do as they were told.

"I doubt we can take this many civvies out of the bunker, ma'am," a Wonderbolt pilot said, approaching Applejack.

"Fleetfoot? What the hell are ya doin' here? Shouldn't ya be at the choppers with the others of your fancy flyin' team?"

"My orders were to come and tell you that we can't take all of them, ma'am. People are going to die, whether we like it or not. I don't, you don't, Captain Spitfire doesn't, but it's gonna happen," Fleetfoot said.

Applejack sighed. "Ah don't care. Take as many as ya can." She replied, watching the crowd slowly move towards the evacuation planes/choppers.

"Women and children first!" Another Wonderbolt, Soarin', yelled, ushering civilians out.

"Ah wish we could really take alla' them," Applejack muttered. "Open the emergency exit! Spit up int'a two organized lines!"

When the steam of people stopped, trying to process what they just heard, Fleetfoot shouted, "You heard the lady! Get moving!"

"This is your life we're talking about here! Move!" Soarin' barked.

"_Now if only __**all'a **__them could get on them planes…_" Applejack thought.

Back at the main entrance of the bunker, Twilight's force of Defenders was quickly dwindling. Men and women fell before her eyes as the swarm of the Infected overcame them. It was to the point where Twilight couldn't stand it anymore.

"Stop!" she screamed. "Get to the evacuation zones! We just can't hold them back!"

The Defenders almost instantaneously turned and ran, aiming behind them and firing as they made their hasty retreat.

Running past the others, Pinkie Pie opened the secondary bulkhead that divided the entrance to the medical wings and living quarters. "Go!" she screamed. "Keep moving!"

When everyone was in, Pinkie pulled a dropped belt-fed machine gun off of the ground. "Seal the doors!"

One of the veteran Defenders quickly moved to complete the order given.

"NO!" Twilight screamed, but she was too late. He hit the button, and the door sealed. Through the glass, they could all see Pinkie Pie valiantly holding her own against the sea of cold hands reaching for her as she unloaded round after round into their bodies.

The veteran Defender sighed. "Come on. She gave her life to buy us some time to run. Let it not be in vain."

Twilight just stood with her mouth agape as Pinkie continued her sustained assault upon the Infected. "But… I… fine," she said after a moment. "Let's go! Move!"

The Defenders did not hesitate once again and continued to run through the halls of the complex.

Confused, Rarity followed the crowd that had amassed in front of her, apparently leading towards the airfield and emergency exit. Clutching tightly to her hands and left leg were the Cutie Mark Crusaders (which doesn't make sense, considering that humans don't get cutie marks…)

"What's going on, Rarity?" Sweetie Belle asked, fear and confusion present in her green eyes.

"I don't quite know, darling," Rarity answered, uncertainty showing through in her voice. "But whatever it is, I'm sure you three will be fine. I shall personally see to it myself."

Leading the three children along, Rarity eventually, spotted Applejack and her older brother ushering the crowd through the airfield gates and the emergency exit.

"Applejack, dear!" Rarity called out.

The woman in question turned and scanned the crowd. Rarity raised her arm into the air, lifting Apple Bloom with it.

Applejack gasped as Apple Bloom called out. "Big sis!"

Slowly, the four of them advanced towards the airfield gateway. And when they finally reached Applejack, she knelt down and received Apple Bloom into her welcoming arms.

"Oh, ya had Big Mac n' me so worried 'bout ya," she said. "Ah didn't see ya when the evacuation started."

"Ah was with Sweetie Belle the entire time, and when the… the… _thingy_ began, Rarity took all o' us here," Apple Bloom replied.

Applejack didn't say anything, instead opting to hug her little sister. And when she finally released her, she looked Rarity dead in the eye.

"Thank ya so much fer' takin' care o' mah little sister," she said, genuine honesty laced into her voice.

"It was only my pleasure, dear. Now, if you would kindly explain to us what exactly is going on here, that would be much appreciated."

Applejack's warm smile melted away, to be replaced with a grim frown. "The bunker's under attack. The Infected are all over." At this, Rarity's blood ran cold. "We've been tryin' ta get everyone out and ta safety."

"Well, I must ask, what are we waiting for, then? Shall we leave?"

"Uh, yeah. Get the girls ta' the choppers out there." Applejack said to Fleetfoot, who had been watching the entire interaction the whole time.

"Yes, ma'am. I'll make sure that they get a spot on the choppers."

"But big sis, what about you and Big Mac?" Apple Bloom asked with concern. "Aren't y'all gonna come with us?"

"Yeah, you too, Rarity! Come on!" Sweetie Belle added, tugging on her older sister's hand.

"I'm afraid not, Sweetie Belle," Rarity said softly. "I must stay here with Applejack and help other people onto the planes. I have to, no matter how much I want to come with you. My conscience will not allow me to stand by and watch other people suffer."

"She's right, Apple Bloom," Applejack agreed. "Mah duty is ta' stay here and help other people, and the same goes fer' Big Mac."

"Come on, girls," Fleetfoot said. "We have to go, now!" She dragged the trio of young girls towards the gates of the airfield.

"But big sis-"Apple Bloom and Sweetie Belle never got the time to finish their protests as they were whisked away.

"I hope they'll be safe," Rarity murmured.

"Don't ya worry none, sugarcube," Applejack replied. "They're in good hands."

Twilight burst through the doors of the medical wing, glancing at the polished white floors and the homey brown walls, making the wing look much like an average, stereotypical hospital.

Quickly, she and the meager remainder of her team ran through the corridors, scanning for survivors that had been left behind when the evacuation started.

Twilight skidded to a stop as she heard quiet sobbing from one of the rooms on her right.

"Hold your position!" she called out to her team. Quietly, she stepped forward and carefully opened the door. In the middle of the room was Fluttershy, who was curled up on a medical bed.

Certain that she was no threat, Twilight stepped up to Fluttershy and rested her hand on her shoulder. "Fluttershy? Fluttershy, come on! We have to go, now!"

Slowly, the timid young woman raised her head. "T-Twilight? W-why are you here?"

"Now's not the best time to explain. Just follow me!" Twilight replied, dragging Fluttershy, who squeaked with protest, up and onto her feet.

Twilight pulled Fluttershy out of the room and into the corridor. Nodding at her team, they continued to race down the stark white halls.

"W-what's going on, Twilight? All I remember are sirens going off and people screaming and running," Fluttershy said in her quiet voice.

"Uh…um… you'll find out later!" Twilight said, making up the excuse. She didn't want to scare the shy woman.

With that, they continued running through the medical wing, bursting through doors and fleeing from the horde of Infected not far behind them.

Finally, after much time of sprinting, Twilight and her team reached the checkpoint that led to the only two ways out of the facility.

Twilight turned towards the veteran Defender that had sealed Pinkie Pie's fate.

"I'm giving your team clearance to board the VIP plane out of here. We need Dr. Fluttershy if we want to find a way to get rid of this threat once and for all."

"W-wait, _my_ team? I thought this was-"

"I don't want to hear it, Corporal. Get your team and Dr. Fluttershy out of here. Now." Upon spotting Applejack, Rarity, and Big Macintosh out in the crowd, she added softly, "And inform Captains Applejack, Rarity, and Big Macintosh that the planes and choppers have full authorization for takeoff."

"… Yes, ma'am."

With that Twilight turned away, pushing through the crowds that crowded in front of the War Room doors.

"But ma'am, what about you?" The veteran called out, but his voice was drowned out in the crowd. Twilight heard him, but she just chose to ignore it.

"Keep it movin' people! It's gonna be crowded on the planes, but you'll have ta' live with it! Come on!" Applejack shouted, trying to pack as many people on the planes as possible. She was screaming things like this for several more minutes before a grizzled-looking man approached her.

"Ma'am, I have specific orders from acting General Twilight Sparkle that me and my team are cleared for immediate VIP seating with special cargo, Dr. Fluttershy."

"She also said that the evac aircraft have full authorization and clearance for takeoff."

"Wait,what? Already? But… Ah suppose… Soarin'!" Applejack called out. Upon hearing his name he turned and pushed through the sea of people to reach Applejack.

"Yes, ma'am?" he asked.

"Take these men escortin' Dr. Fluttershy to the VIP plane," she said. "It's the first plane on the left."

"Yes ma'am," Soarin' said.

"Oh, and Soarin'?" Applejack said.

"Yes, ma'am?"

"Stay on that Celestia-damned plane."

Soarin' smiled slightly. "Come on, you people. That plane's fillin' up fast!" he called out as he lead the tiny group away.

Satisfied that the group would be safe with the lieutenant, Applejack turned to Rarity and Big Mac, both of whom were still urging people on.

"Rarity, Big Mac!" she called out. The people in question turned and began moving towards Applejack.

"Yes, darling? What do you require?" Rarity asked.

"We need ta' get outta here, now. Twilight just gave the order to launch the evac craft. Rapid Fire!"

The Wonderbolt lieutenant in question turned and looked straight at Applejack.

"Get ta' the control tower and let them know that the planes can leave!" Rapid Fire nodded and set off.

Turning back to Rarity and Big Mac, she said, "We should leave now, while we can. Ah'm not sure how much longer the planes are willing to wait fer' us."

With that, the three of them turned to leave the crowded terminal themselves, but not before hearing screams and groans from the rear of the crowd.

Acting General Twilight Sparkle hurried through the darkened corridors of the bunker that led to the War Room. Inside the War Room was her prize-the royal princesses Celestia and Luna.

Bursting through the reinforced steel double-doors, Twilight spotted the two princesses quickly packing items of supposed importance away into small backpack and briefcases. They handed the bags and cases to the unflinching Royal Guards, who, in turn, passed the containers to other guards who carted them down another long hallway.

"Acting General," one of the guards nodded his greeting.

She nodded back, then strode through the many glowing holographic screens and terminal that lined the walls towards the princesses.

"Princess Celestia, Luna, what are you still doing here? We have to get you both out of here, now! The VIP helicopters will be taking off soon!"

"We understand, Twilight. We will use the escape tunnel if we need to," Luna replied. "We will not endanger the lives of others for ourselves."

"But… but if we lose you, the Defenders will surely fail! Both of you are our rallying supports! We'll have no one to lead us!"

Celestia finally stopped what she was doing, turning to face Twilight. "That is why I have full confidence in you and your abilities as our new full-time general, Twilight. You'll be their new beacon of hope in desperate times."

Mouth agape, Twilight stuttered, "Me? But… I'm not… You're…"

Celestia chuckled slightly, a glimmer of old wisdom in her eye. "You may surprise yourself with abilities you may have never known you possessed."

A guard approached the small group just then. "Milady?" he asked.

"What is it? Have the planes taken off yet?" Luna asked anxiously.

"… no, ma'am, but I have come to inform you that the Infected have breached the doors and have begun their intrusion into the civilian crowd at the security checkpoints. I advise that we leave, soon."

"Agh, I knew we should have prepared evacuation procedures earlier, sister! Now we have doomed many to their fates at the cold hands of the undead…" Luna cried out in disbelief.

"Hush, sister. There is nothing we can do now. Flash Sentry?" Celestia said.

The young private swiveled in his chair. "Yes, ma'am? How may I serve you?"

"Arm the warheads. Set the timer for fifteen minutes, no more, no less."

There was a glint of protest and anger in his eyes for just a moment, but he simply nodded. Swiveling around in his chair once again, Flash Sentry faced the screen in front of him and tapped a few icons. "Warheads armed and set for fifteen minutes as requested, ma'am."

"Good. We leave now. Let's go, everyone. Leave everything. Out through the escape tunnel." Celestia said calmly.

The technicians and guards lined up at the door in an orderly fashion, anxiously exiting and hurrying down the dark corridor that led to the outside.

Standing beside the princesses at the front of the said line, Twilight constantly checked over her shoulder to see if anything went wrong, or if the Infected finally caught up to them. Princess Luna noticed this and put her armored hand on Twilight's shoulder.

"There is no need to worry, General. Rest assured, we will all survive."

Twilight shot the Princess of the Night a doubtful look, but then she decided to just focus on the light at the end of the tunnel that was steadily coming closer.

Enveloped in her thoughts, Twilight could never have foreseen the disaster not far behind the end of the line.

Applejack, Big Macintosh, and Rarity ran out of the terminal and onto the airfield tarmac amongst the packed chaos of people trying to flee the oncoming onslaught of undead that was behind them. The cloudy grey skies were filled with aircraft flying away towards the west, and helicopters attempting to pick up more survivors. Attack helicopters also hovered low to the ground near the terminal checkpoint gates, riddling any Infected personnel leaving the terminal with fifty-caliber rounds from their nose-mounted machine guns.

The three friends rushed around, frantically looking for the VIP choppers and planes. They probably would have been the last few survivors on the tarmac if not for Rapid Fire, who saw Applejack, her brother and friend running in confusion.

"Captain Applejack!" he called. "This way!"

Applejack dragged her two companions along over to the lieutenant, who was gathering his fellow surviving Wonderbolts.

"Rapid Fire! Where are the VIP choppers?" Applejack asked.

"They're over here! Come on!" he shouted, taking off at an incredible speed.

Once again, Applejack dragged her companions like ragdolls as she tried to keep Rapid Fire in her line of sight. She only stopped when she felt the weight she had been dragging behind her suddenly decrease. Looking behind her, she saw that she was now only pulling Rarity along with her.

Slowing down, she asked, "Where's Big Mac?" Fear and dread seeped into her voice.

"I don't know! I had his hand, and then…" Rarity replied. But Applejack's brain blocked out all noises from around her when she saw the crowd part behind Rarity, revealing her brother, surrounded by the undead, his flesh being ripped from his bones.

Time around Applejack came to a stop, seeing the pained and confused look on Big Macintosh's face as the Infected consumed his own flesh before his very eyes.

"**NO!**" Applejack screamed, her voice cracking and heavily distorted by the anguish that flooded her body.

"He's gone!" A Wonderbolt said, trying to pull her towards the VIP helicopter that waited ahead. "It's him or us! Let's go, we're almost there!" The woman continued to try and pull Applejack.

"No, we can't leave him! We have ta' go back fer' him!" she protested, struggling against the men and women trying to pull her back.

"I'm sorry, Applejack dear, but we have to go! It's too late! If we turn back now it will be suicide!" Rarity said.

Applejack fell silent as she watched her brother be consumed alive by the things that covered his body. She finally allowed the Wonderbolts to drag her away, watching the tears that streamed down her face splash onto the cracked pavement below.

Apple Bloom, Sweetie Belle, and Scootaloo anxiously scanned the crowd for their family members (excluding Scootaloo, assuming her hero to be on another plane, instead helping her friends search for their loved ones). The endless sea of people moved too quickly for the three girls to keep track of one person's face for long.

Eventually, it was Scootaloo that spotted the remaining Wonderbolts that were helping Applejack and Rarity along through the crowd. "I see them!" she shouted excitedly.

Apple Bloom and Sweetie Belle were quick to rush over to Scootaloo's window.

"Where's Big Mac?" Apple Bloom cried out in dismay as the group steadily approached the helicopter.

"I don't know," Scootaloo said. "I didn't see him with them as they were coming."

"Gee, I really hope he's okay," Sweetie Belle said.

"He better be," Etched with concern, Apple Bloom continued scanning the crowd for hints of her beloved brother, who, unbeknownst to her, was now lost to the sea of cold, grey hands far out on the tarmac.

Applejack was lost in her own little world, memories of her older brother overcoming her mind as she let herself be dragged along by the Wonderbolts ahead of her. The pain associated with the death of her brother still stung, like being slapped in the face.

The memories of the old farm back in Ponyville, Sweet Apple Acres, came back to her as she reminisced. How she missed working on that farm, with the help of Big Mac and little Apple Bloom.

_Apple Bloom!_ Applejack thought, strength flooding her body. She still had something to live for, someone she cared about, and someone that she still needed to protect from the ones that wanted to harm her.

That "someone" was her little sister, Apple Bloom.

Finally, with little effort, Applejack placed her feet on the ground and began to run, matching the pace that the Wonderbolts had been dragging her along at.

Noticing his cargo was lighter than before, one of the Wonderbolts looked back at Applejack.

"Are you alright?" he asked.

"Ah'm fine, thank ya' kindly," Applejack replied.

After a moment of not-so-quiet-silence, the Wonderbolt continued. "I'm sorry," he said. "I lost my brother, too. He went off on a reconnaissance mission, and he and his team never came back."

"Ah'm sorry," Applejack said. At least she had someone to relate to.

The key word was _had_.

With no warning, the Wonderbolt was tackled to the ground by a fast-moving blur, his blood spraying everywhere, staining Applejack's clothing. Glancing to the right, Applejack saw that the attack choppers had run out of ordinance and had ceased firing upon the swarm of undead that burst out of the terminal. The Infected sprinted towards the nearest living crowd they could find, preying upon the helpless civilian as they attempted to make their escape.

Speaking of which, one was heading straight towards Applejack right then. Lunging, the corpse barreled into Applejack, gnashing its teeth as it attempted to bite Applejack's left arm. In response, Applejack struggled and punched the thing straight in the jaw with her free arm, leaving it sprawled out on the pavement not far away. Leaping to her feet, she quickly drew her revolver and shot the corpse dead in the back of the skull.

Looking around in panic, Applejack tried to look for Rarity, who was now probably her only companion here. She found her friend on the ground, struggling against another corpse.

"Applejack!" she cried out upon seeing her friend get to her feet. "Help me, please!"

Rushing forward, Applejack aimed her revolver at the corpse that had leaped onto Rarity. Pulling the trigger, a sense of dread filled her body as she heard a sharp _click_.

Shit.

Applejack knew she had to act quickly. Holstering her revolver, Applejack judged the distance between herself and Rarity. Applejack sprinted as fast as she could in hopes of saving her friend. But before she reached Rarity, she already knew it was too late.

With a burst of incredible strength, the corpse forcefully shoved Rarity's arms to the side and bit down on her shoulder. Drawing its ugly head back up, it dragged a large chunk of Rarity's shoulder along with it.

"_**NO!**_" Applejack screamed. Pushing her legs even harder, she leapt through the air, tackling the corpse on her way back down to the concrete below. Within seconds, Applejack was upon the former man, punching its disfigured face as hard as she could until the skull finally burst into a shower of blood and rotting organic material.

Getting up and whirling around, Applejack rushed over to Rarity's side. She was already growing pale from the amount of blood that she had lost.

"No, no, no, no, no, NO!" Applejack screamed. "You're gonna be fine, sugarcube. Just you wait. We're gonna get ya' outta here and to a safe place, where those doctors or whatever are gonna fix ya' up real good, ya' hear me!"

"Oh, Celestia, it hurts so much," Rarity moaned. "Leave me. There is no point in bringing me with you when all I will do is become a threat. We both know that there is no cure yet. I'm done. I will not endanger the lives of the three young children on that helicopter."

"Please, Rarity. Stay with me. I know it hurts. Just come on!"

"NO!" Rarity screamed. "Just go, and tell Sweetie Belle that her sister loves her." Her voice cracked and faded slightly as she said those words.

"Ah… Ah can't just leave ya' here," Applejack said desperately.

"You have to," Rarity said. "… Oh, the pain… Please, just end it now," she pleaded.

"W-what?" Applejack stuttered. "Ya' want me… ta' _**kill**_ ya'? Now ya know that Ah can't…" Applejack thought it over again upon seeing the pained yet desperate look in her eyes. Deep down, Applejack knew that Rarity was holding back the sudden urge to consume human flesh.

"Alright, sugarcube. I'll see ya' on the other side." Reloading her revolver, Applejack aimed it straight at Rarity's face.

"Thank… thank you so much, Applejack… tell Sweetie… that her sister… loves her…" Rarity's voice faded as she rested her head on the cement.

Slowly, Applejack counted to three, and hesitantly pulled the trigger.

Apple Bloom's eyes were transfixed on the events from outside. Scootaloo was comforting Sweetie Belle, who was crying quietly in the corner of the seats.

"By Celestia…" Apple Bloom said quietly. She became confused when Applejack drew her revolver, reloaded it, and pointed it at Rarity's face. "What're ya' doin', big sis…?"

Apple Bloom jumped when she saw her sister's arm recoil, and the blood splatter the pavement.

"What were ya' thinkin'!?" Apple Bloom shouted.

"What… what's going on?" Sweetie Belle said quietly. She slowly moved to look out the window.

"Uh, nothin'! Just… just watching someone else run!" Apple Bloom plastered a fake smile onto her face while covering the window with her body.

"Why is Rarity laying on the ground without her head?" Scootaloo asked stupidly.

Sweetie Belle's eyes widened to the size of dinner plates. "W-what…?" she stammered.

Scootaloo fell silent for a moment. "Uh…"

In the darkened escape corridor, chaos erupted as the Infected swarmed into the War Room. Technicians and guards destroyed the once-orderly single file line, running through the escape corridor and trampling others in the process.

Twilight rushed out of the tunnel, her view of the princesses gone. Once she was out of the cramped corridor, she stood to the side, searching for the princesses. She would not abandon them here, she thought to herself.

Eventually, Twilight spotted the two princesses exiting the complex, with Celestia's arm draped over Luna's shoulders. Gasping, Twilight ran over to Luna.

"What happened? Is Celestia alright? Are _you_ alright?" Twilight asked.

"I am fine, Twilight. However, the same cannot be said for my sister here. She fell and was trampled by the crowd of men that feared for their lives."

"We have to get both of you away from here, now! Let's go, the chopper is waiting for us!"

Taking Luna's other hand, Twilight led the princesses to the helicopter that was bound to take off at any moment. Hearing groans behind them, Twilight whipped her head around to see the horde of undead that was closing in.

Letting go of Luna's hand, Twilight pushed the princesses ahead.

"Go!" she said. "I'll see if I can hold them off!"

Luna opened her mouth to say something, but closed it and continued to move towards the helicopter.

Pulling a grenade from her belt, Twilight slowly backed away from the undead and pulled the pin. Throwing it, she dove to the ground and covered her head, waiting for the explosion.

Applejack felt a pang of regret wash over her body as her arm recoil. She felt like it was so unfair to just take away her own friend's life like this. Her friend, who was a generous young woman and a caring older sister, which she had just killed.

Thoughts of Sweetie Belle came to her mind as she turned and began running towards the helicopter once again. As she got there, she realized that the aircraft had already begun its takeoff procedures. Swiftly turning, the former farmer broke out in a sprint towards the helicopter, which was already several feet in the air.

Lieutenant Rapid Fire watched Applejack as she ran towards the airborne vehicle. Outstretching his arm, he called out, "Hurry, commander! Grab on!"

Hearing this, Applejack ran even faster. Leaping into the air, she firmly grasped Rapid Fire's hand. He began pulling her up and into the chopper.

From far away, one would think that Applejack would have made it into the vehicle. Alas, this was not the case. With a massive crowd of Infected below the chopper, it would only be a matter of time before they were able to get to the farmer's legs, which were still dangling over the edge of the chopper's hold.

Applejack's heart filled with panic once she felt cold hands grasp her pant legs, bringing her down towards the ground. Even with the power of many Wonderbolt members trying to help her, their strength was no match for the thousands, perhaps millions of corpses that they just hovered over.

"Ya have ta' let go!" Applejack shouted to Rapid Fire. "They're gonna bring ya' down with me if ya' keep tryin' ta' pull me up!"

"No, commander! I can't! We need a good leader to get us through this!"

"_**You're**_ a good leader, Rapid Fire! You can do it! But only if ya' let me go!"

Rapid Fire almost considered relenting. He never got the chance to think, however, as Applejack screamed out in pain, the Infected below beginning to make a meal out of her legs. Seeing the disgusting sights paralyzed Rapid Fire, and he slackened his grip. Applejack let go completely.

"Commander, no!" he shouted, as Applejack was swallowed up by the writhing mass of bodies below. The helicopter began ascending into the cloudy grey skies, leaving behind the fear and confusion, only to give way to the pain of several lost ones that were very special to three young girls.

Empty shell casings flew out of Twilight Sparkle's rifle as she opened fire upon the horde of Infected looming before her. The grenades that she had thrown earlier had little effect on such a massive crowd.

Glancing over her shoulder, Twilight was relieved with the sight of the princesses safe and protected within the helicopter's cargo hold.

"Come, Twilight! We must go, now!" Luna called out.

Twilight dropped her rifle and ran towards the helicopter. But right when she was only several meters away did disaster rear its ugly head.

The fence that separated the VIP helicopter from the airfield gave way, letting another massive crowd of Infected spill through, effectively cutting Twilight off from the chopper.

Drawing her sidearm, Twilight decided to fight to the death. With no viable option to escape, and the chopper unable to come close enough to pick her up safely, she let loose several rounds. In fact, that was all she could unload before the crowds of corpses overwhelmed her completely. The final sight that greeted her eyes before she was torn apart was the helicopter rising into the sky, carrying its vital cargo to another safe place.

And with that, Twilight Sparkle awoke in her darkened quarters in a cold sweat, panting and thinking about what she had just gone through.

**(A/N: My god… that was the longest thing I have ever written for a story.**

**Well, there ya have it, folks! The very first chapter of **_**Contamination Isolation**_**! Hope you guys liked it!**

**Didn't expect it to all be a dream, eh? What, did you think I would kill off almost everyone that fast?**

**Be warned that the next chapter may take a little longer to write, so be prepared.**

**Lastly, just a little bit of trivia for all of you good reviewers out there: I was originally supposed to kill off the CMC in the dream, but I just couldn't bring myself to do it.**

**Reviews will be appreciated, and flames will be used to fend off the Infected.**

**Until next time,**

**-twindragonsx1**

**Devin)**


	3. Chapter 2- Scavengers

**(A/N: Hello, readers. For those who are wondering, the story is set in a post-apocalyptic world where just about 90% of the Equestrian civilian population has been infected with a lethal virus, which generally mutates them into zombies. The Mane Six and princesses Celestia and Luna spearhead a vast majority of the remainder of the Canterlot Royal Guard, as well as some of the civilians of Manhattan.**

No, this is not an OC story. I will try to make this an OC free story, but due to the amount of characters, may have minor characters portrayed by an OC.

If there are any questions on the survivors, plot, or Infected, please let me know by PM or by leaving a review. Thanks!)

_CONTAMINATION ISOLATION_

_Ch. 2_

_SCAVENGERS_

__Twilight breathed heavily, sitting up in her small bunk. The room was shrouded in darkness, save for the light from underneath the doorway. Glancing over at the clock, she saw that it was only 4:38 in the morning.

Shaking her head, she slowly leaned over the edge of the bunk, staring at the lump underneath the covers of the bunk below her. It had appeared that Rainbow Dash was asleep.

Sighing, Twilight climbed down from her bunk. Quickly and quietly, she changed from her nightgown to her uniform, consisting of a white undershirt, lavender coat and a purple skirt. She then turned, and with a few quick strides, she approached the door. She opened the door very slightly, just enough for her to leave out of the room, but not enough to let light filter into the room and rouse Rainbow from her sleep.

Slipping out of the room, Twilight then closed the door and headed down the corridor leading to the cafeteria.

She had always felt safe in these metal halls, even if they were old and rusted. Pipes zigzagged across the walls and ceiling. The cement floor beneath her feet was cracked and worn from years of usage.

But again, she didn't really mind all of that.

She passed several other dormitories and a small repair crew mending a broken pipe before she reached the bulkhead door of the cafeteria. Opening it, she stepped into the open space filled with tables and chairs.

Twilight headed over to the counter lined with empty glass displays, which were supposed to contain whatever was being served for breakfast that day. She rung a small bell on the counter.

"Breakfast isn't ready yet, I'm afraid, but- Oh!"

Twilight bowed her head in greeting. "Sir," she said.

"Ah, good morning, commander. Fine day we have here, isn't it?"

Twilight cracked a smile. "Yes, of course." Obviously, the truth was she hadn't even stepped outside yet.

"You seem troubled, commander. Rough night?"

Twilight nodded slightly.

"Would you like to talk about it?"

"Just nightmares, is all," she replied.

"I see. Everyone's been having nightmares recently. Even your bunk mate, surprisingly enough."

"Really? Rainbow Dash?" Twilight gave a look if disbelief.

"Yup. The one and only." Mr. Cake nodded. "But that aside, what would you like this fine morning, commander?" He chuckled. "Even if there's not much of a selection these days."

"Some toast and some coffee would do just fine, thanks." Twilight said.

"It'll be ready in just a bit."

Nodding, Twilight went and sat at a table, musing over the information she just received. Nightmares could be detrimental to base morale.

From the corner of her eye, Twilight saw a small, thin figure enter the cafeteria. She recognized the person as Fluttershy.

"Fluttershy!" She called out.

The woman in question turned towards Twilight's table and shuffled over to it.

"Oh, um... Good morning, Twilight," she said meekly, taking a seat across from her.

"Hey. So, how's the research going?"

"Um... Okay, I guess..."

"Come on, Fluttershy, I know you can give me a better explanation for that," Twilight sighed. "I mean, you're the head researcher at the medical labs."

"Um... Okay. It's a little slow, partly because of not very many resources, not much staff, and faulty equipment," she replied. "It's also partly because we have no way to test our chemicals safely."

"In other words, you mean a shortage of test subjects," Twilight replied, bluntly.

"... I wouldn't call them that, but if that's what you want to call them, I guess..." Fluttershy said quietly.

"Well, I'm sorry, Fluttershy. I can't do anything about that because I need permission from Princess Celestia before I can do anything. For now, you'll just have to assume they can work and have the scavenger teams test them for you."

"Um...okay..."

After a moment of thinking, Twilight said, "Tell you what. The scavenger teams are supposed to go in an outing today, and it's my turn to lead them. I'll ask the princess if I can bring back at least one subject for testing purposes, alright?"

"Oh, Twilight, I couldn't ask you to do that! What if you get hurt, or what if someone else gets hurt," Fluttershy started to worry. "Or what if it-"

"Fluttershy, stop right there. These men and women are perfectly trained and capable of restraining Infected personnel. Please, just trust me on this," Twilight said.

"Um... Okay. But please be careful, okay? I don't want to see you in the medical bays today..."

"Of course I will," Twilight laughed. "When have I never been careful?"

Silence descended over the table after that. Just as Twilight felt the silence become tense, Mr. Cake called her to the counter.

"Excuse me," she said to Fluttershy. "I'll be back soon."

As Twilight strode over to the counter, Mr. Cake put down a small tarnished metal platter with several pieces of slightly burnt toast, as well as a chipped mug of black coffee.

"Apologies, commander. I know that you like espresso coffee, but it appears that we ran out of espresso beans just yesterday."

Damn. She would have to try and scavenge some more today, then.

"That's alright, Mr. Cake. I'll see if I can find some more today. Thank you." With that, Twilight left the counter and seated herself back at her table, where she ate in uncomfortable silence across from Fluttershy.

After several minutes passed, Twilight finally spoke.

"You know, if you're hungry, why don't you go and ask Mr. Cake to prepare something," she said.

"Oh, no, I'm fine, Twilight. Really. I'm not very hungry right now."

"If you say so," Twilight sighed.

After quickly finishing her meal, Twilight excused herself from the cafeteria, bidding farewell to Fluttershy as she left.

Turning down the hall, Twilight headed down the corridor that led to the war room. Upon reaching the bulkhead doors, she entered a series of eight numbers into the keypad built into the wall nearby. The doors unlocked and parted, revealing the interior of the war room.

Technicians scurried about, carrying stacks of paper and equipment. Others were seated at metal desks studying the heads-up displays before them. In all, it was a crowded mess of data inputs, outputs, and metal.

In the center if it all was Princess Celestia, reading over a report.

Twilight quickly strode past the busy technicians and right up to Celestia. By far, she was the tallest person in the room.

"Um, Princess?" Twilight asked. "Do you have a moment? If it's not a problem?"

Celestia looked up and filed away the report in her uniform's breast pocket.

"Ah, commander. I was not expecting you to be up so early," she said.

"Neither was I," Twilight said, a little louder than she would have liked, an just loud enough for Celestia to hear.

"Then what seems to be the problem, commander?"

Taken by surprise, Twilight stammered, "Um... I... Well... Uh..." She began. Celestia was quiet, awaiting an answer.

With a sigh, Twilight finally relented. "Well, recently, I've been having strange nightmares, disturbing ones, always predicting the downfall of this very facility," she said. "It makes me uneasy."

"I see," the wise former co-ruler of Equestria said. "Try clearing your mind before going to bed. Calm yourself. Don't worry about anything, and just let yourself go." She replied.

"Okay, princess. I'll be sure to do that."

"Now, is there anything else you need?"

Twilight took a deep breath. "Um, I was wondering, since it's my turn to lead the scavenger teams today, if I could also take a reconnaissance team with me."

"Well, why? Are you heading deeper into the city this time?"

"No, no, it's just..." She sighed. "Fluttershy's research team needs test subjects to test their chemicals and prototype cures on. I'm sick of having to always test them on the field, finding out they don't work, and risking ourselves to unnecessary dangers."

After thinking for a quiet minute, Celestia finally replied with a simple yes.

"You're actually fully authorizing for one of the Infected to be in this compound?" Twilight asked, jaw hanging in disbelief.

"Yes. If it's for the process of research and study. However-" Celestia paused. "If you do manage to contain one, do NOT let any civilian see it. Civilian unrest spreads rumors, and rumors will seriously hurt team morale. The fact that Canterlot no longer has the ability to supply us has already lowered morale."

"Yes, ma'am. I'll do my best to ensure that the subject is not seen by anyone other that the recon team."

Celestia sighed. "If that was all? I'm sorry Twilight, but I'm quite busy here." As she said this, she moved aside to reveal a long line of technicians waiting to speak with the princess.

Twilight gasped slightly. "Oh, princess, I'm so sorry! I didn't realize you were so busy!"

"It's alright Twilight. Go get your teams ready. I expect to find a report on my desk tomorrow."

"Yes ,ma'am!" Twilight replied diligently. With that, Twilight turned and exited the war room.

Coming back to her shared room, Twilight knocked on the door to see if Rainbow was awake. After waiting for a solid minute and a half, it was evident that her roommate was not awake.

Unlocking the door with her Level 7 key card, Twilight opened the door, letting the light stream into the darkened room. A lump under the covers stirred slightly, but other than that, did not move.

Groaning, Twilight simply walked over to the bed and harshly threw the blankets off of Rainbow, exposing her body to the cold air of the bunker.

"Hey. Wake up. Now," Twilight said.

When Rainbow did not move, Twilight grabbed one of her roommate's discarded towels and slapped her with it.

"Wake up!" She shouted.

"Ugh... Yeah, yeah, gimme a moment..." Rainbow waved Twilight off.

"No. Get out of bed, now."

After several more minutes of bickering and shouting, Rainbow finally climbed out of bed. Standing up, she straightened her hair out (though it didn't do much).

"Okay. Now that I'm up, whadda ya need?" She said.

"Get dressed and head over to the armory," Twilight replied. "We need a crate of rifles and sidearms down to the airlock in five minutes."

"Ugh, why do I have to do the heavy-lifting? Why can't you get Applejack to do it?"

"Because Applejack isn't a part of the scavenger teams today."

"Wait, this is for the scav teams? Why do you need me for, then? I lead a recon team, not a bunch of scavvies!"

"I need your team today, Dash. Just go and get the weapons."

"... Fine. But I wanna know why you need me and my team when I get down there!"

"Okay. Now go."

Leaving her shared room, Twilight turned and went back to the War Room. Upon entering, she noticed that it was less crowded than before.

From the corner of her eye, she saw the one person she was looking for at the moment, the intercom technician.

"Time Turner!" She called out.

He turned with two mugs of coffee in one hand, a stack of papers in the other, and a plain doughnut in his mouth.

Approaching him, she said, "I need the intercom, just for a few seconds."

He nodded, and led her to his desk. She sat in his chair as he pressed a small green button labeled, "intercom".

"Attention all combat personnel," she began. "Would reconnaissance team Gamma-8 and scavenger teams Nu-6 and Mu-7 please gear up in the armory and head down to the airlock. You have five minutes." With that, she got up from the chair. Thanking Time Turner, she then left the War Room.

From the War Room, she headed to the armory, passing several other soldiers also heading to the same place.

Upon arriving at the thick blast door, she pulled out her keycard and slotted it into the keycard reader near the door. And with a great heave, the doors slowly opened.

Removing her keycard, Twilight and the other soldiers headed inside, gearing up for another day of scrounging.

"Alright people, quiet down!" Twilight shouted. She, Rainbow Dash, and the soldiers if Gamma-8, Nu-6, and Mu-7 stood at the doors of the airlock as Twilight prepared to relay their mission objectives.

"Today's scavenger trip is special, because not only do we need supplies, but we need one live specimen of the Infected," she said. As she expected, this caused a wave of unrest to sweep over the soldiers.

Murmurs of insanity whispered from soldier to soldier, and questions arose of the purpose of their goal.

"Are you crazy, Twilight?" Rainbow asked. "Why? The thing could kill a lot of people if we lost control of it!" Soldiers shouted and vocalized their own opinions.

"What if we can't secure one?"

"I don't want to do this..."

"It's a threat to everyone here!"

"I have a wife and kids!"

Sighing, Twilight screamed, "Everyone shut up!"

Each and every complaint stopped right then and there.

"The medical team needs a live subject to test their prototype chemicals on. If we don't give this to them, we will never find an effective way to test them. The faster they do this, the less men we will lose. So if you don't do this, we'll never find an effective cure fast enough for us to use. So how about you all put your fears aside and be the soldiers I need you to be!"

Silence settled over the room for quite some time.

She turned towards the soldier nearest to the door control panel, Lyra Heartstrings.

"Open the door," she said sternly.

The doors opened, and the teams filed out into the wastes.

The once-great city of Manhattan loomed over the horizon, a forest of fire, glass, and metal. The skyline was dominated by crumbling skyscrapers and towers, a reminder of what the city once was. The ominous gray sky let few rays of light through, shining down on the destroyed roads that led to the city.

"Alright people, you know what to do. Pack it up into our armored carriers," Rainbow said.

Just beyond the great blast doors of the airlock was a small garage, which contained numerous vehicles that the Manhattan branch of survivors had struggled to maintain for the last few months.

As the merged squads neared the small building, a Mu-7 soldier, Bon Bon, flipped open a small keypad next to the steel doors. She punched in a few numbers, and the shuttered doors began sliding open.

Stored within the garage were 5 armored personnel transports, each with a mounted machine gun at the top.  
"Let's go, people! I want to be home in time for lunch!" Twilight barked.

The vehicles' engines roared as the teams rode off towards the burning city.

**(A/N: Well, this was a particularly long chapter after a long wait. Which I apologize for in advance, as I was busy this summer. Now that school's started up again, I pray that you will never have to wait as long.**

Also, I typed this on my phone, so it seems long here. I hope it's just as long on the computer!

If you have any suggestions for the story, please PM me and let me know. Thanks!

Reviews would be appreciated.)


	4. Chapter 3- Swarm

**(A/N: Um, there's not much I can say about this chapter. The action starts here, but that's it.**

In other news, A Derpy King Boo and I are working on a collaborative story together. It's still in the works, but of course, when it's finished you should check it out.

Reviews are appreciated.)

_CONTAMINATION ISOLATION  
Ch. 3  
Swarm_

The small convoy of armored transports made their way down the ruined highway towards the city. They carefully drove past fallen debris and abandoned cars that littered the road. The gray skies above let in little sunlight, so the transports' headlights were on to navigate the darkness.

Helicopters piloted by the remaining Wonderbolts flew overhead, spotlights scanning the roads. They were here to help on the scavenger mission and warn the teams of incoming threats.

In the lead vehicle, Twilight Sparkle sat in the passenger seat, with Rainbow Dash driving.

As she looked out the window, Twilight let her mind wander. She thought about her life before the virus, and how it was able to spread so quickly. She thought of the other last stronghold the survivors had up in Canterlot. Her brother led the resistance there along with Princess Cadence.

A crack on the road caused Twilight to bump her head on the window, effectively jolting her out of her thoughts.

Taking notice, Rainbow asked her,"Are you alright?"

Shaking her head slightly, Twilight replied with a "yes".

After a few seconds more of awkward silence, Rainbow spoke.

"Good thing those creeps up in Canterlot still got those satellites working, huh?"

"Yeah," Twilight replied. "Without them, you wouldn't know where you're driving."

"Hey, what's that supposed to mean?" Rainbow asked looking at Twilight.

"Oh, nothing, nothing. Just pay attention to the road and drive. Wouldn't want to crash now," Twilight deliberately said.

"Fine," Rainbow shot back with a mock attitude.

It was a quiet and uneventful trip into the city after that, with only the GPS occasionally chiming out directions.

Within minutes, the convoy had left the freeway and turned onto the main roads, buildings and other structures ravaged by the elements. Many buildings had crumbled completely, becoming nothing more than piles of rubble.

"Alright egghead, we're here. Tell us what to do." Rainbow said, slowing down their transport.

Pulling a handheld radio attached to the control console in front of her, Twilight clicked it on and spoke into it.

"Okay people, listen up," she began.

"Team Nu-6, take the east sector of the city. Sweep that area for supplies and survivors."

"Team Mu-7, I want you on the west side. Pick up any and all supplies. We all know that area is hot with the Infected, so stay sharp, and be quiet."

"In the active event of an emergency, such as the threat of Infected Swarms, pull out immediately and engage in protocol Kappa R9-27. For those of you who do not know what this is, it is to disengage and retreat to an area away from the bunker. Once you are certain that the Infected are no longer a threat, you are to make your way back to base using an alternative route."

Looking in the mirror, Twilight watched as just about three quarters of the convoy peeled away from the formation, moving left and right respectively.

"As for Gamma-8," Twilight began once more.

"You're with me. We're heading south."

Gamma-8 drove down the road towards the heart of the city, the helicopters watching for any movement.

Pulling out the radio again, Twilight contacted the choppers.

"Grey Hornet, do you have a visual on Central Plaza, I repeat do you have a visual on Central Plaza, please respond, over," she spoke.

A few seconds passed. Then, a choppy and whiny signal patched through, filled with white noise.

"We have a visual on Central Plaza, over. About a quarter mile left. You are to be forewarned, commander. There is a large group of zed down there. Please advise, over," the lead chopper pilot replied.

"Lieutenant, your orders are to fly overhead and open fire on any and all hostiles, I repeat, open fire on any and all hostiles."

"Yes, ma'am." In the background, Twilight could hear the co-pilot radioing the other choppers before the signal cut out.

Twilight looked up into the dark, hazy grey sky, watching the helicopters fly ahead. Soon enough, automatic machine gun fire could be heard.

By the time Gamma-8 got to the scene, there was nothing left but bodies riddled with bullets littering the area.

Contacting the helicopters again, Twilight congratulated them on a job well done.

The team moved on, heading farther south, something that no team had done before.

"Are you sure 'bout this, Twilight? No one's been here before. We don't know what's back here," Rainbow said, an uneasy tone to her voice.

"Yes, I'm sure. Everywhere else has been depleted of their resources, and the east and west sides of the city are almost devoid of anything but rubble. This is the only other place we haven't checked. I don't like it either, but we have no choice."

"Alright, fine. But If we end up busting our chops back to base early, I'm blaming this on you."

"Okay. Fine."

A patchy signal came through the radio again. "Gamma-8, you have a large number of hostiles on their way towards you from the west. Prepare to engage."

"Oh, shit..." Rainbow said quietly.

The entirety of Gamma-8 pulled over as gunners popped the hatches on top of the transports and loaded the mounted guns. Soldiers disembarked their transports and readied their weapons.

Twilight radioed the choppers. "We have contact! Weapons free!"

Twilight aimed down the sights of her rifle as the oncoming wave of undead steadily approached. Pulling the trigger, she shot one, two, three of her targets, each one scoring her a kill.

Just left of her, Rainbow pulled the trigger and sprayed the area with automatic weapons fire, taking down quite a few of the Infected. The attack choppers overhead opened up with their barrage of missile fire, leaving smoldering craters in the ground, dirt spraying everywhere.

But even with the heavy resistance that they faced, the Infected kept coming, crawling over the debris that blocked their way. Ever so slowly they advanced upon the small team before them.

The radio on Twilight's belt flared to life.

"Incoming tangos from the south. Commander, I advise that we get the hell out of here, now!"

The wall of Infected slammed into the first line of soldiers, overwhelming them, tearing them apart in a gruesome, bloody mess. The screams of pain and despair pierced Twilight's very soul.

"I repeat, incoming tangoed from the south. ETA five minutes."

"Alright people, let's go! We have to get out of here, now! Move!" Twilight screamed.

The machine guns on the transports grunted, emptying their belts into the mob of undead ahead of them. The helicopters provided suppression fire as the soldiers piled themselves into the transports. The tires of the transports squealed on the cracked asphalt as they sped off, quickly losing the Infected nipping at their heels.

Inside the last transport, Twilight leaned her head back into the seat, settling into the soft leather. Across from her sat Rainbow Dash.

"Nice job, genius," she spat, a tone of disgust laced into her raspy voice. "You almost got us killed, AND you did manage to kill a bunch of perfectly good men. We didn't even pick up supplies!"

"Need I remind you who you're talking to, Lieutenant?" Twilight said sternly. Deep down inside, she knew that it was her fault. She was the one who gave the order to engage.

It was a silent five minutes before Twilight picked up her radio and tried to contact squad Mu-7.

"Squad Mu-7, this is Commander Twilight Sparkle. What's your status, over," she said.

All she got was the hiss of static.

"I repeat, this is Commander Twilight Sparkle. If you can hear this, please respond, over."

More static filtered through the radio.

Sighing, Twilight radioed the helicopters.

"Grey Hornet, I want a helicopter to recon the west side of the city. Squad Mu-7 is unresponsive."

A burst of static was part of her reply. "Yes ma'am, heading there now."

Staring out the window, Twilight watched the grey skies as a helicopter headed west. She feared for the soldiers of Mu-7, because she simply could not afford to waste any more lives.

The chopper that belonged to the pilot Rapid Fire, callsign Grey Hornet, flew over the ruined city towards the west. The burning buildings below showed no sign of Mu-7.

His helicopter flew low over the city, weaving in and out of the destroyed buildings and glided across the cracked pavement. Abandoned vehicles littered the worn streets, and he constantly had to look out for obstacles in his path.

However, Rapid Fire noticed that the farther away from the city he flew, the more signs of conflict appeared. The exterior walls of the buildings were pockmarked with bullet holes, and armored vehicles were left abandoned in a hurry in the middle of the road.

He kept flying, hoping for a sign of survivors. It'd be a shame to return to the commander empty-handed, after all.

Soon, it was evident, by the growing number of Infected that were shuffling about on the streets, that Mu-7 was close by. Rapid Fire was nearing the edge of the city limits, and if he didn't find the squad soon, he was just going to forget it and return to base.

And just as he was seriously considering that thought, he finally found the squad, outnumbered and outgunned.

Commander Twilight Sparkle sat in the War Room, anxiously awaiting a response from Grey Hornet. She absentmindedly twiddled her thumbs, mentally reviewing her actions earlier that day.

"Hi!"

Enveloped in her own thoughts, Twilight never noticed the pink mass of energy pop up in front of her. Giving a surprised shout, she kicked her chair backwards, nearly falling over.

After recovering from her shock, Twilight took a deep breath and said, "Pinkie, what did I tell you about startling me like that?"

"Oh, I'm sorry, Twilight, but I saw you looking really, really sad today after you came back from your scavvie trip, and so I followed you here just to try to cheer you up and make you happy, because everyone looks better when they're happy, right? Because whenever I see someone upset, that means something's wrong, and when something's wrong that person's not happy, and I love to make everyone happy, because everyone looks better when-"

Twilight cut her off right there. "Yes, Pinkie, I get it."

"Okay then! So why don't ya tell me what's wrong?"

Twilight sighed. "Look, Pinkie, as much as I'd love to stay and chat about my feelings, I am waiting on a very important call-"

This time Twilight was cut off by her radio. A scratchy voice filtered through the speaker. "Commander, do you copy, over? Commander, if you can hear me, I have located Squad Mu-7. I repeat, I have located Squad Mu-7, do you copy?"

Fishing out her radio from her utility belt, Twilight held a button down as she replied to Grey Hornet.  
"Solid copy, Grey Hornet. What's going on down there?"

"The remainder of the squad is holed up in a tower 8 miles away from their last recorded position," he replied, "and we have a Code Brown Infected swarm on their asses."

Fear traveled down Twilight's spine as she spoke back into the radio. "What did you say, Lieutenant? Did you say "Code Brown"?"

"Yes, ma'am, we have the leading edge of Legion M-86 nipping at their heels. Advise immediate reinforcements and a full site-lockdown."

"Solid copy, soldier. Come on home."

"Grey Hornet out." The radio clicked off as Twilight slipped it back onto her belt.

Running to the alert console, Twilight hit the yellow "panic button". Immediately after that, she ran over to the intercom console, clicked a green button, and spoke into the microphone.

"This is Commander Twilight Sparkle. We have a Level-5 threat incoming, Infected Swarm Category level-6. Full site-lockdown initiated. All fireteams are to report to the armories to load up, and are then expected to carry out Directive-096D. Fireteams Alpha and Bravo, meet me at the airfield in Hangar-08C. Let's go people, on the double! Twilight out."

Twilight turned to address Pinkie. "I need you on Fireteam Zulu. As of now, you are the commander of all heavy-ordinance fireteams. Understood?"

Pinkie snapped a quick salute in response. "Ma'am, yes ma'am! I won't let you down!"

"Good," Twilight said as she pivoted on her heel and exited the War Room, hearing klaxon alarms blaring, heavy footsteps in the halls, and the massive bulkhead doors sealing behind her.

**(A/N: Finally done with Chapter 3. I'm quite satisfied with the final product, if I do say so myself.**

Reviews-appreciated. Flames-not appreciated.

Until next time,  
twindragonsx1  
-Devin)


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